R4RNA: An R package for RNA visualization and analysis

A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.

AuthorDaniel Lai, Irmtraud Meyer <irmtraud.meyer@cantab.net>
Date of publicationNone
MaintainerDaniel Lai <jujubix@cs.ubc.ca>
LicenseGPL-3
Version1.2.0
http://www.e-rna.org/r-chie/

View on Bioconductor

Functions

alignmentCanonical Man page
alignmentConservation Man page
alignmentCovariation Man page
alignmentPercentGaps Man page
as.helix Man page
baseConservation Man page
basepairCanonical Man page
basepairConservation Man page
basepairCovariation Man page
basepairFrequency Man page
blankPlot Man page
collapseHelix Man page
colourByBasepairFrequency Man page
colourByCanonical Man page
colourByConservation Man page
colourByCount Man page
colourByCovariation Man page
colourByUnknottedGroups Man page
colourByValue Man page
defaultPalette Man page
expandHelix Man page
fasta Man page
helix Man page
helixCanonical Man page
helixConservation Man page
helixCovariation Man page
helixToBpseq Man page
helixToConnect Man page
helixToVienna Man page
isConflictingHelix Man page
isDuplicatingHelix Man page
is.helix Man page
isOverlappingHelix Man page
known Man page
logceiling Man page
logfloor Man page
logseq Man page
maxHeight Man page
parseBracket Man page
plotArc Man page
plotArcs Man page
plotCovariance Man page
plotDoubleCovariance Man page
plotDoubleHelix Man page
plotHelix Man page
plotOverlapCovariance Man page
plotOverlapHelix Man page
R4RNA Man page
R4RNA-package Man page
readBpseq Man page
readConnect Man page
readHelix Man page
readVienna Man page
structureMismatchScore Man page
unknottedGroups Man page
viennaToHelix Man page
writeHelix Man page

Files

R4RNA/DESCRIPTION
R4RNA/NAMESPACE
R4RNA/NEWS
R4RNA/R
R4RNA/R/io.R R4RNA/R/misc.R R4RNA/R/plot.R R4RNA/R/stats.R
R4RNA/build
R4RNA/build/vignette.rds
R4RNA/data
R4RNA/data/helix.RData
R4RNA/inst
R4RNA/inst/CITATION
R4RNA/inst/doc
R4RNA/inst/doc/R4RNA.R
R4RNA/inst/doc/R4RNA.Rnw
R4RNA/inst/doc/R4RNA.pdf
R4RNA/inst/extdata
R4RNA/inst/extdata/bpseq.txt
R4RNA/inst/extdata/connect.txt
R4RNA/inst/extdata/fasta.txt
R4RNA/inst/extdata/helix.txt
R4RNA/inst/extdata/vienna.txt
R4RNA/man
R4RNA/man/R4RNA-package.Rd R4RNA/man/alignmentStatistics.Rd R4RNA/man/as.helix.Rd R4RNA/man/basepairFrequency.Rd R4RNA/man/blankPlot.Rd R4RNA/man/colourHelices.Rd R4RNA/man/expandCollapseHelix.Rd R4RNA/man/helix.Rd R4RNA/man/logicalHelix.Rd R4RNA/man/logseq.Rd R4RNA/man/plotCovariance.Rd R4RNA/man/plotHelix.Rd R4RNA/man/readStructure.Rd R4RNA/man/structureMismatchScore.Rd R4RNA/man/unknottedGroups.Rd R4RNA/man/viennaToHelix.Rd R4RNA/man/writeHelix.Rd
R4RNA/vignettes
R4RNA/vignettes/R4RNA.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.